Setup

Data Description & Quality Assessment

*GC content of each library showing uneven and 'spikey' patterns. Peaks on the RHS indicate potential incomplete rRNA removal, whilst the other peaks indicate possible excessive PCR cycles and high levels of duplicated sequences.*

GC content of each library showing uneven and ‘spikey’ patterns. Peaks on the RHS indicate potential incomplete rRNA removal, whilst the other peaks indicate possible excessive PCR cycles and high levels of duplicated sequences.

*Estimated duplication levels within each sample. Higher than expected sequence duplication rates were observed, particularly for sequences present greater than 10,000 times. Sample 179_F and 187_F were of particular concern, however this is also suggestive of incomplete rRNA removal*

Estimated duplication levels within each sample. Higher than expected sequence duplication rates were observed, particularly for sequences present greater than 10,000 times. Sample 179_F and 187_F were of particular concern, however this is also suggestive of incomplete rRNA removal

*STAR Alignment summary showing very low levels of unique alignments, which is again suggestive of incomplete rRNA removal. Uniquely mapping reads are within the range usually seen after summarising to genes, indicating that final gene-level counts may be a little lower than is optimal.*

STAR Alignment summary showing very low levels of unique alignments, which is again suggestive of incomplete rRNA removal. Uniquely mapping reads are within the range usually seen after summarising to genes, indicating that final gene-level counts may be a little lower than is optimal.

After assignment to transcripts, the library sizes ranged between 6,954,273 and 14,565,667 reads

Initial Analysis

PCA with colours indicating treatment group and point sizes indicating sample weights. A trend from left to right along PC1 tracked somewhat with library size, with all points along PC1 appearing in order of library size for each respective treatment group. Point sizes are proportional to sample weights.

*Correlation between library size and PC1. A simple regression line is also shown for illustrative purposes*

Correlation between library size and PC1. A simple regression line is also shown for illustrative purposes

Differentially Expressed Genes

Differentially expressed (DE) genes were detected using a slight variation from the common null hypothesis. Instead of testing \(H_0: \log FC = 0\) which tests for the point value zero, the null hypothesis was defined as being within the range [\(-\tau, \tau\)], with \(\tau\) set at the default value of \(\log_2 1.2\). This additionally saves filtering any detected DE based on fold-change as is common practice in many workflows.

\[ H_0: |\log FC| \leq \tau \\ vs \\ H_A: |\log FC| > \tau \]

  • After analysis, 2 genes were found to be differentially expressed using an FDR of 0.05.
  • Using a less stringent FDR threshold of 20.0% gave weak-to-moderate support for 18 genes as potentially DE.
Top 18 most highly-ranked genes when sorting by p-value. This represents an FDR of up to20.0%.logFC > 0 indicates up regulation in diabetic samples relative to control
ID Name logFC AveExpr t P.Value FDR Location
ENSRNOG00000047551 Pnpla2 -7.193 0.1297 -13.05 3.334e-06 0.02846 1:213997709-214002815:(+)
ENSRNOG00000050004 LOC100909761 6.555 -1.417 12.52 4.326e-06 0.02846 9:37727942-37747514:(+)
ENSRNOG00000032832 Mmp10 3.502 2.164 8.791 3.768e-05 0.1653 8:5734348-5742243:(+)
ENSRNOG00000032626 Mmp3 3.614 4.589 8.206 5.899e-05 0.1738 8:5676665-5698579:(+)
ENSRNOG00000002802 Cxcl1 4.896 1.902 7.857 8.384e-05 0.1738 14:18743685-18745457:(-)
ENSRNOG00000010278 Il6 4.791 0.1518 7.82 8.594e-05 0.1738 4:3043231-3047807:(+)
ENSRNOG00000060849 Rcor2 -5.115 -1.303 -7.711 9.531e-05 0.1738 1:222519615-222524779:(+)
ENSRNOG00000000239 Ccl7 2.753 2.899 7.269 0.0001174 0.1738 10:69423086-69424979:(+)
ENSRNOG00000007545 Angptl4 1.852 3.859 7.063 0.0001256 0.1738 7:18627808-18634079:(-)
ENSRNOG00000024705 Rarres2 2.478 4.591 6.78 0.0001754 0.1738 4:78205812-78208767:(-)
ENSRNOG00000015992 Ccl20 4.46 0.1233 6.935 0.0001788 0.1738 9:88918433-88921001:(+)
ENSRNOG00000048321 Tnfsf8 2.08 2.527 6.608 0.0001953 0.1738 5:79664765-79691258:(-)
ENSRNOG00000020953 Ms4a7 1.993 2.448 6.573 0.0001993 0.1738 1:227490777-227506822:(-)
ENSRNOG00000062228 LOC100359515 4.667 0.8863 6.776 0.0002085 0.1738 10:64762907-64790306:(-)
ENSRNOG00000002792 Cxcl2 7.728 2.716 6.865 0.0002128 0.1738 14:18731378-18733391:(-)
ENSRNOG00000022839 Ifit3 3.29 6.303 6.642 0.0002153 0.1738 1:252906234-252911382:(+)
ENSRNOG00000028043 Cxcl3 6.557 2.794 6.723 0.0002349 0.1738 14:18820168-18839595:(-)
ENSRNOG00000016812 Adamts16 3.1 0.7835 6.518 0.0002378 0.1738 1:35067490-35198939:(+)
*Average expression against logFC. Confidently significant genes (FDR < 0.05) are indicated in red, whilst others are labelled to an FDR of 20.0%*

Average expression against logFC. Confidently significant genes (FDR < 0.05) are indicated in red, whilst others are labelled to an FDR of 20.0%

*Volcano plot with confidently significant genes shown in red. Genes to an FDR of20.0%are labelled.*

Volcano plot with confidently significant genes shown in red. Genes to an FDR of20.0%are labelled.

*Expression values for genes to an FDR of 20.0%. Genes are shown in order of significance.*

Expression values for genes to an FDR of 20.0%. Genes are shown in order of significance.

Gene Set Enrichment

Given the relatively small number of DE genes, the most suitable enrichment analysis was chosen to be GSEA as this works on a ranked list with no requirement for formal consideration of genes as differentially expressed. This approach walks through a ranked list and checks to see if genes with a given gene-set are clustered at either end of the ranked list. If no correlation between the gene-set and the experiment is evident, they should be evenly spread throughout the list. Otherwise they could reasonably be expected to show directional bias. As this is a fairly broad view analysis, gene sets were chosen as defined for human EntrezGene identifiers, then these were mapped to Ensembl rat identifiers. All gene-sets are described at the Broad Institute

Four gene sets were chosen:

  • Hallmark gene-sets (k = 50): These are a small number of well defined, or high-level gene sets
  • C2 Curated gene-sets (k = 4762): Gene sets curated from various sources such as online pathway databases, the biomedical literature, and knowledge of domain experts.
  • C5 GO gene-sets (k = 5917): Gene sets that contain genes annotated by the same GO term
  • C7 Immunologic Signature gene-sets (k = 4872): Gene sets that represent cell states and perturbations within the immune system. The signatures were generated by manual curation of published studies in human and mouse immunology.

Hallmark Gene Sets

Enriched Hallmark gene-sets using a Bonferroni-adjusted p-value < 0.01 for stringency. The normalised enrichment score indicates which end of the ranked list appeared to be enriched, with negative values indicating the down regulated genes. The number of genes in the gene-set are also indicated, as are the number of genes at the point of maximum enrichment. Any genes in the geneset which appeared in the most highly ranked 100 DE genes are shown to give a broad picture of which genes may be playing a role.
Pathway NES \(p\) \(p_{adj}\) size sizeAtMax DE
HALLMARK_INTERFERON_GAMMA_RESPONSE 1.672 1.153e-06 5.763e-05 181 37 Il6,Ccl7,Ifit3,Ptgs2,C1s,Isg15,Sod2,Tnfaip6
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION 1.828 1.155e-06 5.777e-05 178 84 Mmp3,Il6,Cxcl6,Tgfbi
HALLMARK_TNFA_SIGNALING_VIA_NFKB 1.929 1.158e-06 5.791e-05 175 87 Il6,Tlr2,Cxcl6,Il1b,Ptgs2,Sod2,Junb,Tnfaip6,G0s2
HALLMARK_MYOGENESIS 1.781 1.165e-06 5.824e-05 168 72 LOC108348074,Mylpf,Myh8,Tnni2,Myoz1,Myl1,Myh1,Ckm
HALLMARK_COMPLEMENT 1.697 1.17e-06 5.848e-05 163 36 Il6,Ctsl,C1s,Ctss
HALLMARK_INFLAMMATORY_RESPONSE 1.934 1.171e-06 5.854e-05 162 59 Il6,Ccl7,Tlr2,Cxcl6,Il1b,Has2,Il1r1,Tnfaip6
HALLMARK_COAGULATION 1.777 1.268e-06 6.342e-05 92 29 Mmp3,Ctsl,Cfi,C1s
HALLMARK_HEME_METABOLISM -2.071 7.776e-06 0.0003888 187 80
HALLMARK_MYC_TARGETS_V1 -1.799 7.98e-06 0.000399 193 45
HALLMARK_E2F_TARGETS -2.282 8.261e-06 0.000413 200 94
HALLMARK_G2M_CHECKPOINT -2.003 8.303e-06 0.0004152 201 70
HALLMARK_HYPOXIA 1.56 6.441e-05 0.003221 184 57 Il6,Angptl4,Errfi1,LOC100911515,Tgfbi
HALLMARK_MITOTIC_SPINDLE -1.529 0.0001079 0.005397 201 31
HALLMARK_IL6_JAK_STAT3_SIGNALING 1.669 0.0001088 0.005442 79 24 Il6,Ccl7,Tlr2,Il1b,Il1r2,Il1r1,Cxcl13
*Enrichment score for the most highly ranked hallmark geneset*

Enrichment score for the most highly ranked hallmark geneset

C2 Curated Gene Sets

As this was a larger database of gene-sets, only those with between 15 & 500 genes were tested. To obtain greater statistical precision the number of permutations was increased to \(1\times10^6\).

Enriched C2 gene-sets using a Bonferroni-adjusted p-value < 0.01 for stringency. The normalised enrichment score indicates which end of the ranked list appeared to be enriched, with negative values indicating the down regulated genes. The number of genes in the gene-set are also indicated, as are the number of genes at the point of maximum enrichment. Any genes in the geneset which appeared in the most highly ranked 100 DE genes are shown to give a broad picture of which genes may be playing a role.
Pathway NES \(p\) \(p_{adj}\) size sizeAtMax DE
REN_ALVEOLAR_RHABDOMYOSARCOMA_DN 1.771 1.052e-06 0.003661 400 117 S100a6,Cttn,Ptges,C1s,Tspo,Tgfbi,Rhoc
LIM_MAMMARY_STEM_CELL_UP 1.577 1.052e-06 0.003662 398 130 Il6,Rarres2,Medag,Il1b,Ptgs2,Has2,Adamts1
FOSTER_TOLERANT_MACROPHAGE_DN 1.522 1.055e-06 0.003672 386 83 Il6,Tnfsf8,Il1b,LOC497963,Errfi1,Ptgs2,Junb,Nfkbiz
NABA_MATRISOME_ASSOCIATED 1.756 1.057e-06 0.003677 380 156 Mmp3,Il6,Ccl7,Angptl4,Tnfsf8,Adamts16,Cxcl6,S100a6,Ctsl,C1qtnf7,Il1b,Slpi,Adamts15,Masp1,Adamts1,Cxcl13,Ctss,Pcsk5,LOC100911486,Ccl3
HAN_SATB1_TARGETS_DN 1.521 1.058e-06 0.00368 376 81 Il6,Ifit3,Il1b,Ptgs2,Slpi,Tspo,Tgfbi,Pcsk5
CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_DN 1.623 1.058e-06 0.003681 375 116 Ifit3,Tlr2,Cfi,Ptgs2,Slpi,C1s,Tgfbi
RUTELLA_RESPONSE_TO_HGF_UP 1.563 1.059e-06 0.003685 372 106 Il1b,Il1r2,C1s,Sod2,Il1r1,Tnfaip6,Ccl3
BOQUEST_STEM_CELL_CULTURED_VS_FRESH_UP 1.678 1.059e-06 0.003686 371 120 Angptl4,Cfi,LOC108348074,Prg4,Sod2,Junb,Tnfaip6,Ctss
DELYS_THYROID_CANCER_UP 1.61 1.064e-06 0.003701 355 105 Tlr2,Cttn,Slpi,Has2,Tnfaip6,Ctss,G0s2,Tspo,Ccl3
LINDGREN_BLADDER_CANCER_CLUSTER_2B 1.616 1.065e-06 0.003706 351 96 Rarres2,LOC108348074,C1s,Nfkbiz
SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP 1.737 1.076e-06 0.003744 318 117 Mmp3,Rarres2,LOC108348074,C1s,Il1r1,Tnfaip6,Ctss,Tgfbi
RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN 1.633 1.082e-06 0.003767 300 97 S100a6,Adamts15
PASINI_SUZ12_TARGETS_DN 1.598 1.092e-06 0.0038 277 106 S100a6,Errfi1
WANG_SMARCE1_TARGETS_UP 1.794 1.117e-06 0.003888 229 88 Ifit3,Cfi,LOC108348074,Car4,C1s,Prg4,Il1r1,Tgfbi
HOSHIDA_LIVER_CANCER_SUBCLASS_S1 1.662 1.121e-06 0.003901 223 61 LOC108348074,Ctss,Ccl3
BOQUEST_STEM_CELL_UP 1.677 1.125e-06 0.003914 217 85 C1s,Tnfaip6
VERHAAK_GLIOBLASTOMA_MESENCHYMAL 1.708 1.126e-06 0.00392 215 90 Tlr2,Il1r1,Tgfbi
MCLACHLAN_DENTAL_CARIES_UP 1.676 1.13e-06 0.003933 210 72 Il6,Cfi,Il1b,LOC108348074,Ptgs2,Slpi,Sod2,Cxcl13,Tnfaip6,Ctss,G0s2,Ccl3
MARKEY_RB1_ACUTE_LOF_DN 1.67 1.135e-06 0.00395 203 56 Mmp3,Ccl7,Ifit3,Isg15,Sod2,Tgfbi,Pcsk5,Ccl3
PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP 1.725 1.149e-06 0.003997 186 68 Rarres2,LOC108348074,C1s,Adamts1
ZWANG_CLASS_3_TRANSIENTLY_INDUCED_BY_EGF 1.686 1.151e-06 0.004006 183 68 Il6,Il1b,Ptgs2,Junb,Nfkbiz
ZHANG_RESPONSE_TO_IKK_INHIBITOR_AND_TNF_UP 1.745 1.155e-06 0.004021 178 59 Ifit3,Tlr2,Il1b,Il1r2,Sod2,Tnfaip6,G0s2,Nfkbiz
BROWN_MYELOID_CELL_DEVELOPMENT_UP 1.864 1.181e-06 0.004109 152 48 Tlr2,S100a6,Il1b,Il1r2,Junb,Ctss,Tgfbi
GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_UP 1.733 1.2e-06 0.004175 135 50 Angptl4,Errfi1,Vwa1,LOC100911515,Nfkbiz
NABA_ECM_REGULATORS 1.77 1.201e-06 0.00418 134 61 Mmp3,Adamts16,Ctsl,Slpi,Adamts15,Masp1,Adamts1,Ctss,Pcsk5
MIKKELSEN_MEF_LCP_WITH_H3K4ME3 1.829 1.232e-06 0.004289 112 51 Ccl7,Masp1
ALTEMEIER_RESPONSE_TO_LPS_WITH_MECHANICAL_VENTILATION 1.985 1.235e-06 0.004298 110 50 Il6,Tlr2,Cxcl6,Il1b,Il1r2,Isg15,Sod2,Junb,Nfkbiz,Ccl3
HOLLERN_EMT_BREAST_TUMOR_UP 1.803 1.247e-06 0.004339 103 39 Medag
GALINDO_IMMUNE_RESPONSE_TO_ENTEROTOXIN 1.86 1.293e-06 0.0045 80 42 Il1b,Errfi1,Ptgs2,Junb,Ccl3
HESS_TARGETS_OF_HOXA9_AND_MEIS1_DN 1.826 1.309e-06 0.004556 73 32 Tlr2,Il1b,Il1r2,Car4,Ctss,Tgfbi
SANA_TNF_SIGNALING_UP 1.874 1.337e-06 0.004653 63 22 Mmp3,Ccl7,Tlr2,Cxcl6,C1s,Sod2
LINDSTEDT_DENDRITIC_CELL_MATURATION_A 1.888 1.375e-06 0.004786 51 25 Il6,Tlr2,Il1b,Isg15,Sod2,Ccl3
RICKMAN_HEAD_AND_NECK_CANCER_F 1.929 1.394e-06 0.004851 46 34 LOC100909761,Mylpf,Mybpc2,Tnni2,Myl1,Myh1,Ckm
THUM_SYSTOLIC_HEART_FAILURE_UP 1.506 2.118e-06 0.007371 371 98 Cfi,C1s,Ctss
ROZANOV_MMP14_TARGETS_UP 1.617 2.229e-06 0.007756 234 79 Tlr2,Aldh18a1,Il1r2,Errfi1,Has2,Il1r1
VECCHI_GASTRIC_CANCER_ADVANCED_VS_EARLY_UP 1.705 2.377e-06 0.008271 145 55 Il6,Tlr2,LOC108348074,Sod2,Tnfaip6
GROSS_HYPOXIA_VIA_ELK3_DN 1.708 2.381e-06 0.008287 143 48 Il6,Cxcl6,Errfi1,Ptgs2,Slpi,Vwa1
JECHLINGER_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_UP 1.805 2.662e-06 0.009265 65 24 Ifit3,Cxcl6,Slpi,Isg15
NAKAYAMA_SOFT_TISSUE_TUMORS_PCA1_UP 1.823 2.668e-06 0.009286 64 33 S100a6,C1s,Tnfaip6
*Enrichment score for the most highly ranked C2 geneset* As this peak was relatively far from the significantly DE genes, this is not a partiularly compelling result

Enrichment score for the most highly ranked C2 geneset As this peak was relatively far from the significantly DE genes, this is not a partiularly compelling result

C5 GO Gene Sets

Enriched C5 gene-sets using a Bonferroni-adjusted p-value < 0.01 for stringency. The normalised enrichment score indicates which end of the ranked list appeared to be enriched, with negative values indicating the down regulated genes. The number of genes in the gene-set are also indicated, as are the number of genes at the point of maximum enrichment. Any genes in the geneset which appeared in the most highly ranked 100 DE genes are shown to give a broad picture of which genes may be playing a role.
Pathway NES \(p\) \(p_{adj}\) size sizeAtMax DE
GO_CELLULAR_RESPONSE_TO_CYTOKINE_STIMULUS 1.659 1.041e-06 0.004111 452 125 Il6,Ccl7,Ifit3,Cxcl6,Il1b,Il1r2,Arg1,LOC497963,Has2,Isg15,Il1r1,Cxcl13,Ccl3
GO_CALCIUM_ION_BINDING 1.534 1.046e-06 0.004129 427 138 Mmp3,S100a6,Mylpf,C1s,Masp1,Myl1,LOC100911692,LOC100911486
GO_INNATE_IMMUNE_RESPONSE 1.679 1.046e-06 0.004132 423 110 Ccl7,Ifit3,Tlr2,Cfi,LOC497963,Slpi,C1s,Isg15,Masp1,Ccl3
GO_IMMUNE_EFFECTOR_PROCESS 1.6 1.059e-06 0.004183 368 83 Il6,Ifit3,Cxcl6,Cfi,LOC103692716,C1s,Isg15,Masp1,Ifit1bl,Ccl3
GO_ACTIN_CYTOSKELETON 1.598 1.062e-06 0.004192 361 66 LOC100909761,Mylpf,Cttn,Myh8,Abra,Mybpc2,Tnni2,Myoz1,Myl1,Myh1
GO_RESPONSE_TO_BACTERIUM 1.584 1.068e-06 0.004217 341 104 Il6,Tnfsf8,Tlr2,Cxcl6,Il1b,Arg1,LOC497963,Ptgs2,Ptges,Slpi,Isg15,Junb,Cxcl13,Tspo,Ccl3
GO_CYTOKINE_MEDIATED_SIGNALING_PATHWAY 1.726 1.074e-06 0.004243 321 92 Il6,Ccl7,Ifit3,Cxcl6,Il1b,Il1r2,Isg15,Il1r1,Cxcl13,Ccl3
GO_REGULATION_OF_SYSTEM_PROCESS 1.634 1.075e-06 0.004244 320 102 Il6,Il1b,Agtr2,Cttn,LOC497963,Errfi1,Ptgs2,LOC103692716,Tnni2,Ccl3
GO_INFLAMMATORY_RESPONSE 1.67 1.075e-06 0.004247 318 105 Il6,Ccl7,Rarres2,Tlr2,Cxcl6,Il1b,Agtr2,Ptgs2,Ptges,Cxcl13,Tnfaip6,Nfkbiz,Ccl3
GO_REGULATION_OF_RESPONSE_TO_WOUNDING 1.769 1.08e-06 0.004263 308 97 Il6,Ccl7,Tlr2,Cfi,Il1b,LOC497963,Ptgs2,Masp1,Il1r1,Tnfaip6,Wfdc1,Ccl3
GO_EXTRACELLULAR_MATRIX 1.783 1.086e-06 0.004287 292 123 Mmp3,Angptl4,Rarres2,Adamts16,LOC108348074,Slpi,LOC103692716,Adamts15,Vwa1,Adamts1,Tgfbi
GO_RESPONSE_TO_MOLECULE_OF_BACTERIAL_ORIGIN 1.682 1.105e-06 0.004365 250 79 Il6,Tlr2,Cxcl6,Il1b,Arg1,LOC497963,Ptgs2,Ptges,Slpi,Junb,Cxcl13,Tspo,Ccl3
GO_PROTEINACEOUS_EXTRACELLULAR_MATRIX 1.768 1.113e-06 0.004393 237 101 Mmp3,Angptl4,Adamts16,LOC108348074,Adamts15,Vwa1,Adamts1,Tgfbi
GO_REGULATION_OF_INFLAMMATORY_RESPONSE 1.85 1.124e-06 0.004439 218 79 Il6,Ccl7,Tlr2,Cfi,Il1b,LOC497963,Ptgs2,Masp1,Il1r1,Tnfaip6,Wfdc1,Ccl3
GO_MUSCLE_SYSTEM_PROCESS 1.925 1.141e-06 0.004507 194 73 LOC100909761,Il1b,Agtr2,Mylpf,Myh8,LOC103692716,Mybpc2,Tnni2,Myl1,Myh1
GO_REGULATION_OF_ERK1_AND_ERK2_CASCADE 1.709 1.159e-06 0.004578 173 46 Il6,Ccl7,Il1b,Errfi1,Scimp,Ccl3
GO_CONTRACTILE_FIBER 1.925 1.169e-06 0.004616 163 63 LOC100909761,Mylpf,Myh8,Abra,Tnni2,Myl1,Myh1
GO_MUSCLE_CONTRACTION 1.973 1.172e-06 0.004629 160 67 LOC100909761,Mylpf,Myh8,LOC103692716,Mybpc2,Tnni2,Myl1,Myh1
GO_CELLULAR_RESPONSE_TO_BIOTIC_STIMULUS 1.717 1.195e-06 0.00472 139 42 Il6,Tlr2,Il1b,Arg1,LOC497963,Tspo,Ccl3
GO_DEFENSE_RESPONSE_TO_VIRUS 1.734 1.214e-06 0.004793 125 26 Il6,Ifit3,Isg15,Ifit1bl
GO_POSITIVE_REGULATION_OF_RESPONSE_TO_WOUNDING 1.829 1.236e-06 0.004882 110 41 Il6,Ccl7,Tlr2,Il1b,Ptgs2,Ccl3
GO_RESPONSE_TO_INTERFERON_GAMMA 1.9 1.244e-06 0.004913 105 38 Ccl7,LOC497963,Ccl3
GO_CELLULAR_RESPONSE_TO_INTERFERON_GAMMA 1.93 1.284e-06 0.00507 84 33 Ccl7,LOC497963,Ccl3
GO_LEUKOCYTE_CHEMOTAXIS 1.813 1.301e-06 0.005137 77 33 Il6,Ccl7,Il1b,Cxcl13,Ccl3
GO_POSITIVE_REGULATION_OF_INFLAMMATORY_RESPONSE 1.874 1.306e-06 0.005156 75 35 Il6,Ccl7,Tlr2,Il1b,Ptgs2,Ccl3
GO_CELLULAR_RESPONSE_TO_INTERLEUKIN_1 1.888 1.335e-06 0.005272 64 31 Il6,Ccl7,Has2,Il1r1,Ccl3
GO_PEPTIDASE_ACTIVITY 1.524 2.099e-06 0.008291 408 96 Mmp3,Adamts16,Ctsl,Cfi,C1s,Adamts15,Masp1,Adamts1,Ctss,Pcsk5
GO_POSITIVE_REGULATION_OF_DEFENSE_RESPONSE 1.602 2.171e-06 0.008573 292 66 Il6,Ccl7,Tlr2,Il1b,Ptgs2,Ctss,Ccl3
GO_POSITIVE_REGULATION_OF_ERK1_AND_ERK2_CASCADE 1.709 2.442e-06 0.009645 120 38 Il6,Ccl7,Il1b,Scimp,Ccl3
GO_REGULATION_OF_CYTOKINE_SECRETION 1.737 2.505e-06 0.009894 100 38 Il6,Tlr2,Il1b,Agtr2,Ccl3
*Enrichment score for the most highly ranked C2 geneset* As this peak was relatively far from the significantly DE genes, this is not a partiularly compelling result

Enrichment score for the most highly ranked C2 geneset As this peak was relatively far from the significantly DE genes, this is not a partiularly compelling result

C7 Immunologic Signatures

Enriched C7 gene-sets using a Bonferroni-adjusted p-value < 0.01 for stringency. The normalised enrichment score indicates which end of the ranked list appeared to be enriched, with negative values indicating the down regulated genes. The number of genes in the gene-set are also indicated, as are the number of genes at the point of maximum enrichment. Any genes in the geneset which appeared in the most highly ranked 100 DE genes are shown to give a broad picture of which genes may be playing a role.
Pathway NES \(p\) \(p_{adj}\) size sizeAtMax DE
GSE42021_TCONV_PLN_VS_TREG_PRECURSORS_THYMUS_DN 1.785 1.144e-06 0.005574 192 49 Ccl7,Angptl4,Il1b,Errfi1,Ptgs2,Ptges,LOC103692716,Junb,Nfkbiz
GSE22935_WT_VS_MYD88_KO_MACROPHAGE_UP 1.733 1.145e-06 0.005577 191 58 Ptgs2
GSE42021_TREG_PLN_VS_CD24INT_TREG_THYMUS_UP 1.837 1.146e-06 0.005582 190 59 Il1b,Errfi1,Ptgs2,Ptges,LOC103692716,Junb,Nfkbiz
GSE18281_SUBCAPSULAR_VS_CENTRAL_CORTICAL_REGION_OF_THYMUS_DN 1.687 1.147e-06 0.005589 188 53 Ifit3,Cxcl6,Ifit1bl,Nfkbiz
GSE27434_WT_VS_DNMT1_KO_TREG_DN 1.809 1.149e-06 0.005598 186 44 Ccl7,Il1b,Errfi1,Ptgs2,LOC103692716,Junb,Nfkbiz
GSE14769_UNSTIM_VS_60MIN_LPS_BMDM_DN 1.705 1.15e-06 0.005602 185 53 Ccl7,Tlr2,Il1b,Errfi1,Ptgs2,Sod2
GSE3039_ALPHAALPHA_VS_ALPHABETA_CD8_TCELL_UP 1.726 1.151e-06 0.005606 184 52 Il6,Tlr2,Ctsl,Ptges,LOC100911515
GSE14769_UNSTIM_VS_40MIN_LPS_BMDM_DN 1.757 1.153e-06 0.005619 181 53 Ccl7,Tlr2,Errfi1,Ptgs2,Junb,Nfkbiz
GSE45365_NK_CELL_VS_CD11B_DC_DN 1.785 1.155e-06 0.005627 179 54 Il6,Il1b,Ptges,Junb,Nfkbiz
GSE14769_UNSTIM_VS_80MIN_LPS_BMDM_DN 1.766 1.156e-06 0.005631 178 59 Tlr2,Il1b,Isg15,Sod2,Adamts1
GSE19198_CTRL_VS_IL21_TREATED_TCELL_24H_UP 1.762 1.156e-06 0.005631 178 54 Mmp3,Il6,Ccl7,Errfi1,Sod2
GSE46606_UNSTIM_VS_CD40L_IL2_IL5_1DAY_STIMULATED_IRF4HIGH_SORTED_BCELL_DN 1.724 1.156e-06 0.005631 178 42 Il6,Il1b,Errfi1,Ptgs2,Nfkbiz
GSE18281_CORTICAL_VS_MEDULLARY_THYMOCYTE_UP 1.731 1.158e-06 0.00564 176 58 Ifit3,Cxcl6,Arg1,Ptgs2,Slpi,Isg15,Ifit1bl,Ctss
GSE42021_TREG_PLN_VS_CD24HI_TREG_THYMUS_UP 1.827 1.159e-06 0.005648 174 55 Ccl7,Il1b,Errfi1,Ptgs2,LOC103692716,Junb,Nfkbiz
GSE32986_CURDLAN_HIGHDOSE_VS_GMCSF_AND_CURDLAN_HIGHDOSE_STIM_DC_DN 1.719 1.16e-06 0.005652 173 58 Rarres2,Tlr2,Il1b,Ptgs2,Isg15,Sod2,Junb,Nfkbiz
GSE9316_IL6_KO_VS_IFNG_KO_INVIVO_EXPANDED_CD4_TCELL_DN 1.831 1.161e-06 0.005657 172 57 Ccl7,Ptges,Tspo,Nfkbiz
GSE42021_CD24HI_TREG_VS_CD24HI_TCONV_THYMUS_DN 1.805 1.162e-06 0.005662 171 59 Ccl7,Il1b,Errfi1,Ptgs2,LOC103692716,Junb,Nfkbiz
GSE9988_LOW_LPS_VS_CTRL_TREATED_MONOCYTE_UP 1.682 1.179e-06 0.005743 154 63 Il6,Il1b,Errfi1,Ptgs2,Sod2,Tnfaip6,G0s2,Nfkbiz,Ccl3
GSE9988_ANTI_TREM1_VS_ANTI_TREM1_AND_LPS_MONOCYTE_DN 1.683 1.184e-06 0.005771 149 58 Il6,Il1b,Ptgs2,Sod2,Tnfaip6,G0s2,Nfkbiz
GSE2585_CD80_HIGH_VS_LOW_AIRE_KO_MTEC_UP 1.728 1.184e-06 0.005771 149 58 Il6,LOC497963,C1s,LOC100911515,Tgfbi,Nfkbiz
GSE9601_NFKB_INHIBITOR_VS_PI3K_INHIBITOR_TREATED_HCMV_INF_MONOCYTE_DN 1.914 1.184e-06 0.005771 149 50 Mmp3,Ccl7,Ifit3,Medag,Ptgs2,Sod2
GSE21360_SECONDARY_VS_QUATERNARY_MEMORY_CD8_TCELL_UP 1.791 1.184e-06 0.005771 149 61 Il6,Ccl7,Il1b,LOC497963,Ptgs2,Ptges,Sod2,Nfkbiz,Ccl3
GSE36888_UNTREATED_VS_IL2_TREATED_TCELL_17H_DN 1.712 1.191e-06 0.005803 143 44 Il6,Tlr2,Cxcl6,Ptgs2,Ptges,Sod2,Tnfaip6,G0s2,Nfkbiz
GSE36891_POLYIC_TLR3_VS_PAM_TLR2_STIM_PERITONEAL_MACROPHAGE_UP 1.832 1.241e-06 0.006047 107 42 Mmp3,Il6,Ccl7,Ptgs2,Adamts1,Junb,Nfkbiz
*Enrichment score for the most highly ranked C2 geneset* As this peak was relatively far from the significantly DE genes, this is not a partiularly compelling result

Enrichment score for the most highly ranked C2 geneset As this peak was relatively far from the significantly DE genes, this is not a partiularly compelling result

Session Info

R version 3.5.2 (2018-12-20)

**Platform:** x86_64-pc-linux-gnu (64-bit)

locale: LC_CTYPE=en_AU.UTF-8, LC_NUMERIC=C, LC_TIME=en_AU.UTF-8, LC_COLLATE=en_AU.UTF-8, LC_MONETARY=en_AU.UTF-8, LC_MESSAGES=en_AU.UTF-8, LC_PAPER=en_AU.UTF-8, LC_NAME=C, LC_ADDRESS=C, LC_TELEPHONE=C, LC_MEASUREMENT=en_AU.UTF-8 and LC_IDENTIFICATION=C

attached base packages: stats4, parallel, stats, graphics, grDevices, utils, datasets, methods and base

other attached packages: fgsea(v.1.8.0), Rcpp(v.1.0.1), ggrepel(v.0.8.0), plyranges(v.1.2.0), rtracklayer(v.1.42.2), GenomicRanges(v.1.34.0), GenomeInfoDb(v.1.18.2), IRanges(v.2.16.0), S4Vectors(v.0.20.1), scales(v.1.0.0), ngsReports(v.0.99.7), BiocGenerics(v.0.28.0), pander(v.0.6.3), magrittr(v.1.5), forcats(v.0.4.0), stringr(v.1.4.0), dplyr(v.0.8.0.1), purrr(v.0.3.2), readr(v.1.3.1), tidyr(v.0.8.3), tibble(v.2.1.1), ggplot2(v.3.1.0), tidyverse(v.1.2.1), edgeR(v.3.24.3) and limma(v.3.38.3)

loaded via a namespace (and not attached): nlme(v.3.1-137), bitops(v.1.0-6), matrixStats(v.0.54.0), lubridate(v.1.7.4), RColorBrewer(v.1.1-2), httr(v.1.4.0), tools(v.3.5.2), backports(v.1.1.3), R6(v.2.4.0), lazyeval(v.0.2.2), colorspace(v.1.4-1), withr(v.2.1.2), gridExtra(v.2.3), tidyselect(v.0.2.5), compiler(v.3.5.2), cli(v.1.1.0), rvest(v.0.3.2), Biobase(v.2.42.0), Cairo(v.1.5-9), xml2(v.1.2.0), DelayedArray(v.0.8.0), plotly(v.4.8.0), ggdendro(v.0.1-20), labeling(v.0.3), digest(v.0.6.18), Rsamtools(v.1.34.1), rmarkdown(v.1.12), XVector(v.0.22.0), pkgconfig(v.2.0.2), htmltools(v.0.3.6), highr(v.0.8), htmlwidgets(v.1.3), rlang(v.0.3.2), readxl(v.1.3.1), rstudioapi(v.0.10), shiny(v.1.2.0), generics(v.0.0.2), zoo(v.1.8-5), hwriter(v.1.3.2), jsonlite(v.1.6), crosstalk(v.1.0.0), BiocParallel(v.1.16.6), RCurl(v.1.95-4.12), GenomeInfoDbData(v.1.2.0), Matrix(v.1.2-17), Rhdf5lib(v.1.4.3), munsell(v.0.5.0), stringi(v.1.4.3), yaml(v.2.2.0), MASS(v.7.3-51.1), SummarizedExperiment(v.1.12.0), zlibbioc(v.1.28.0), rhdf5(v.2.26.2), plyr(v.1.8.4), grid(v.3.5.2), promises(v.1.0.1), crayon(v.1.3.4), lattice(v.0.20-38), Biostrings(v.2.50.2), haven(v.2.1.0), hms(v.0.4.2), locfit(v.1.5-9.1), knitr(v.1.22), pillar(v.1.3.1), fastmatch(v.1.1-0), XML(v.3.98-1.19), glue(v.1.3.1), evaluate(v.0.13), ShortRead(v.1.40.0), latticeExtra(v.0.6-28), data.table(v.1.12.0), modelr(v.0.1.4), httpuv(v.1.5.0), cellranger(v.1.1.0), gtable(v.0.3.0), assertthat(v.0.2.1), xfun(v.0.5), mime(v.0.6), xtable(v.1.8-3), broom(v.0.5.1), later(v.0.8.0), viridisLite(v.0.3.0), truncnorm(v.1.0-8) and GenomicAlignments(v.1.18.1)